Although Shiela's exact wish had been that her commands would be followed, her suggestion that Mikey be a girl, in her mind, had been a command, because that was the way that she was taught to give commands, and the stone recognized that this was effectively another form of language with its own distinct rules, and as such, any statement or question that Shiela spoke in regards to a command, would be interpreted as a command.
And as such, Mikey had just been given a command to 'be a girl'. How would that work out?